Hello sophiazotou,
You could try a different way of getting rid of the rows with zeros and see if it works out for you in this situation.
I am suggesting this because i cannot visualize how the selection for the entire data is happening when you select filter, especially because after a certain number of rows, the filter doe not usually give the correct result. I have seen this especially when i have data in more than 10k rows.
To use this, so a test run with a copy of your workbook because this has no undo.
under the file menu, under the "info" sub menu, you will see the option for Inspect Workbook.
Click on Check for Issues. Select the Inspect Document option. That will open the "Document Inspector" then Click on the "Inspect" button. a list of options will appear. While you scroll down the list of options, you will come across an option titled ‘Hidden Rows and Columns’. Select the “Remove All” option. this will permanently remove all the hidden rows.[ hence the need to work on a copy, just in case] Click on the ‘Close’ button. go back to the worksheet and remove all applied filters
With the above, what you will have hidden is rows with "ZERO" quantities. Try it and let me know how it goes.